Related Experiment Video
Updated: May 10, 2026
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
BeEP Server: Using evolutionary information for quality assessment of protein structure models.
Nicolas Palopoli1, Esteban Lanzarotti, Gustavo Parisi
1Departamento de Ciencia y Tecnologia, Universidad Nacional de Quilmes, B1876BXD, Bernal, Buenos Aires, Argentina.
Nucleic Acids Research
|June 5, 2013
Summary
The BeEP Server ranks protein structure models using evolutionary information, not just structure or energy. This method identifies native-like protein structures by analyzing evolutionary patterns in homologous proteins.
Area of Science:
- Computational Biology
- Bioinformatics
- Structural Biology
Background:
- Protein structure prediction is a complex challenge.
- Existing methods often rely on structural or energetic evaluations.
- A novel approach utilizing evolutionary information can enhance model assessment.
Purpose of the Study:
- To introduce the BeEP Server as an online resource for protein structure prediction.
- To present a new method for ranking protein structural models using evolutionary data.
- To evaluate the effectiveness of the BeEP method in identifying native-like structures.
Main Methods:
- The BeEP Server employs evolutionary information to rank protein models.
- It utilizes substitution patterns from homologous proteins to build site-specific matrices.
- Maximum likelihood calculations assess matrix suitability and derive position-specific scores.
Main Results:
- BeEP successfully discriminates between protein structural models.
- The method can select native-like structures from submitted models.
- BeEP's evolutionary approach aids in exploring the native state's conformational ensemble.
Conclusions:
- The BeEP Server offers a unique approach to protein structure model assessment.
- Evolutionary information provides a valuable criterion for ranking structural models.
- BeEP demonstrates potential for improving the accuracy and scope of protein structure prediction.
Related Concept Videos
01:29Protein Folding Quality Check in the RER
ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
02:15Protein and Protein Structure
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
A protein's shape is critical to its function. For example, an enzyme can...
02:15Protein and Protein Structures
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
A protein's shape is critical to its function. For example, an enzyme can...
01:24Protein Organization
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
The primary structure of a protein is its amino acid sequence.
02:47Protein Families
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key locations, protein...
02:54Evolutionary Relationships through Genome Comparisons
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...